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Seeing as it gets to the point of loading uBoot, one might reasonable presume that AT91BootStrap is loading successfully into SRAM (you could checksum that), and that your real problem is how you are initializing your SDRAM/DDR, clocks and system.
I'd look very carefully at the SDRAM circuit, the configuration and timings being used. Check you have the geometry, refresh, and initialization sequences correct for the chips you are using, and the speed is as suitable.
I'd look very carefully at the PLL settings, and the stability of the clocks being generated/used by the memory and peripherals.
I'm not hugely familiar with the G45, but other SAM9's come up at 48 MHZ, and then your code in AT91BootStrap gear it up to maximal speed, and initializes the SDRAM/DDR.
Check also your NAND timings on the external bus when running at the higher speed.
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